Not sure I understand the question, but you should be able to do that easily by using contourf and scatter.
For example, let's say you have some xy data (n x 2) and you want to plot certain points on a contourf:
n = 100; n points
ind = [20,40,60,94]; %points to plot
xy = randi([10 20],n,2)
contourf(peaks);hold on
scatter(xy(ind,1),xy(ind,2),[],'k')
